Rs2542151

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Orientationplus
Geno Mag Summary
(G;G) 2x risk for Crohn's; 1.6x for T1D
(G;T) 1.3x risk for Crohn's; 1.3x for T1D
(T;T) 0 normal
ReferenceGRCh38 38.1/141
Chromosome18
Position12779948
GenePTPN2
is asnp
is mentioned by
dbSNPrs2542151
Exacrs2542151
PheGenIrs2542151
nextbiors2542151
hapmaprs2542151
1000 genomesrs2542151
hgdprs2542151
ensemblrs2542151
gopubmedrs2542151
geneviewrs2542151
scholarrs2542151
googlers2542151
pharmgkbrs2542151
gwascentralrs2542151
openSNPrs2542151
23andMers2542151
23andMe allrs2542151
SNP Nexus

SNPshotrs2542151
SNPdbers2542151
MSV3drs2542151
GMAF0.1561
? (G;G) (G;T) (T;T) 28
rs2542151 has been reported in a large study to be associated with Crohn's disease.

The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.3 (CI 1.14-1.48), and for homozygotes, 2.01 (CI 1.46-2.76). [PMID 17554300OA-icon.png]

rs2542151 has been reported in the same study to be associated with type-1 diabetes. The risk allele (oriented to the dbSNP entry) is (G); the odds ratio associated with heterozygotes is 1.30 (CI 1.15-1.47), and for homozygotes, 1.62 (CI 1.17-2.24). [PMID 17554300OA-icon.png]

In an expanded follow-up study of >6,000 controls and 6,000 patients, the heterozygote odds ratio for this SNP was recalculated to be 1.30 (CI 1.22–1.40). [PMID 17554260OA-icon.png]

GWAS
SNP rs2542151
PubMedID [PMID 17554260OA-icon.png]
Condition Type 1 diabetes
Gene PTPN2
Risk Allele C
pValue 1.00E-014
OR 1.3
95% CI 1.22-1.40


GWAS snp
PMID [PMID 18978792OA-icon.png]
Trait Type 1 diabetes
Title Meta-analysis of genome-wide association study data identifies additional type 1 diabetes risk loci
Risk Allele C
P-val 9E-8
Odds Ratio NR NR
GWAS snp
PMID [PMID 18587394OA-icon.png]
Trait Crohn's disease
Title Genome-wide assocation defines more than 30 distinct susceptibility loci for Crohn's disease
Risk Allele G
P-val 4.9999999999999999E-17
Odds Ratio 1.35 [NR]
GWAS snp
PMID [PMID 17554261OA-icon.png]
Trait Crohn's disease
Title Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility
Risk Allele
P-val 2.9999999999999997E-8
Odds Ratio 1.15 [1.00-1.32]

[PMID 19565500OA-icon.png] Variants in TNFAIP3, STAT4, and C12orf30 loci associated with multiple autoimmune diseases are also associated with juvenile idiopathic arthritis

OMIM612354
DescINFLAMMATORY BOWEL DISEASE 21; IBD21
Variant
Relatedalso
OMIM222100
DescDIABETES MELLITUS, INSULIN-DEPENDENT; IDDM
Variant
Relatedalso



[PMID 19953089] Differences in genetic background between active smokers, passive smokers, and non-smokers with Crohn's disease




[PMID 21246196] A polymorphism in PTPN2 gene is associated with an earlier onset of type 1 diabetes

GWAS snp
PMID [PMID 21829393OA-icon.png]
Trait
Title Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases.
Risk Allele G
P-val 4E-13
Odds Ratio 1.3000 [NR]


[PMID 22377701OA-icon.png] PTPN2 is associated with Crohn's disease and its expression is regulated by NKX2-3.


[PMID 18224312OA-icon.png] Pharmacogenetics: data, concepts and tools to improve drug discovery and drug treatment.


[PMID 18252225OA-icon.png] On the use of general control samples for genome-wide association studies: genetic matching highlights causal variants.


[PMID 18423522OA-icon.png] Estimating odds ratios in genome scans: an approximate conditional likelihood approach.


[PMID 18438406OA-icon.png] Genetic determinants of ulcerative colitis include the ECM1 locus and five loci implicated in Crohn's disease.


[PMID 18533027OA-icon.png] Worldwide population differentiation at disease-associated SNPs.


[PMID 18853133OA-icon.png] Gene variants influencing measures of inflammation or predisposing to autoimmune and inflammatory diseases are not associated with the risk of type 2 diabetes.


[PMID 19140132OA-icon.png] Unbiased estimation of odds ratios: combining genomewide association scans with replication studies.


[PMID 19359276OA-icon.png] Identification of AF4/FMR2 family, member 3 (AFF3) as a novel rheumatoid arthritis susceptibility locus and confirmation of two further pan-autoimmune susceptibility genes.


[PMID 19474294OA-icon.png] Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.


[PMID 19639606OA-icon.png] Correcting "winner's curse" in odds ratios from genomewide association findings for major complex human diseases.


[PMID 19776214OA-icon.png] SimCT: a generic tool to visualize ontology-based relationships for biological objects.


[PMID 19915572OA-icon.png] Genome-wide association study of ulcerative colitis identifies three new susceptibility loci, including the HNF4A region.


[PMID 20369022OA-icon.png] Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations.


[PMID 20403149] PTPN2 but not PTPN22 is associated with Crohn's disease in a New Zealand population.


[PMID 21304977OA-icon.png] An investigation of genome-wide studies reported susceptibility loci for ulcerative colitis shows limited replication in north Indians.


[PMID 22021207] Crohn's disease-associated polymorphism within the PTPN2 gene affects muramyl-dipeptide-induced cytokine secretion and autophagy.


[PMID 22426692] Confirmation of three inflammatory bowel disease susceptibility loci in a Chinese cohort.


GET Evidence
rs2542151
aa_change
aa_change_short
impact pathogenic
qualified_impact Insufficiently evaluated pathogenic
overall_frequency 0.898438
summary



[PMID 24127071] Associations between PTPN2 polymorphisms and susceptibility to ulcerative colitis and Crohn's disease: a meta-analysis


[PMID 23518806] Association between the PTPN2 gene and Crohn's disease: dissection of potential causal variants


[PMID 24480412] PTPN2 rs1893217 single-nucleotide polymorphism is associated with risk of Behçet's disease in a Chinese Han population


[PMID 25460303] Epistasis amongst PTPN2 and genes of the vitamin D pathway contributes to risk of juvenile idiopathic arthritis